Poll: What times are best for you for office hours?

Today is different

Ava will hold office hours from 5:00pm - 6:00pm EST.

Office hours will always be held at the same Zoom link.

RStudio is an Integrated Development Environment (IDE) for R

• It helps the user effectively use R
• Makes things easier
• Is NOT a dropdown statistical tool (such as Stata)
  • See Rcmdr or Radiant

_[source]

RStudio used to be the name of a company that is now called Posit.

Easier working with R

• Syntax highlighting, code completion, and smart indentation
• Easily manage multiple working directories and projects

More information

• Workspace browser and data viewer
• Plot history, zooming, and flexible image and file export
• Integrated R help and documentation
• Searchable command history

You must open a file first to save code to open the editor. These include for example R Scripts or R Markdown.

1. The Source/Editor: “Analysis” Script + Interactive Exploration
   • Static copy of what you did (reproducibility)
   • Top by default
2. The R Console: “interprets” whatever you type
   • Calculator
   • Try things out interactively, then add to your editor
   • Bottom by default

• Where files open to
• Have R code and comments in them
• Can highlight and press (CMD+Enter (Mac) or Ctrl+Enter (Windows)) to run the code

In a .R file (we call a script), code is saved on your disk

• Where code is executed (where things happen)
• You can type here for things interactively to test code
• Code is not saved on your disk

Super useful “cheat sheet”: https://github.com/rstudio/cheatsheets/raw/master/rstudio-ide.pdf

To make an R Markdown file: click the green plus button -> R Markdown. We will do this together soon! It will look like this with text in it, unlike a script.

Although people will use scripts often, and they are good for more programmatic purposes, we generally don’t recommend them for Public Health Researchers.

For data analyses, R Markdown files are generally superior because they allow you to check your code and write more info about your code.

If RStudio doesn’t look the way you want (or like our RStudio), then do:

RStudio –> Preferences –> Pane Layout

• Tells you what objects are in R
• What exists in memory/what is loaded?/what did I read in?

History

• Shows previous commands. Good to look at for debugging, but don’t rely on it.
  Instead use RMarkdown!
• Also type the “up” key in the Console to scroll through previous commands

• Files - shows the files on your computer of the directory you are working in
• Viewer - can view data or R objects
• Help - shows help of R commands
• Plots - pictures and figures
• Packages - list of R packages that are loaded in memory

💻 RStudio Lab

To do this lab we need to:

1. Download the file at the link above by clicking on the link or typing in: https://jhudatascience.org/intro_to_r/modules/RStudio/lab/RStudio_Lab.Rmd

(Also on the website schedule page - Lab for day 1) 2) Find the downloaded file on your computer 3) Open the file in RStudio

This may require finding your downloads on your computer.

Recall that these videos can help:

If you have a PC: https://youtu.be/we6vwB7DsNU

If you have a Mac: https://www.youtube.com/watch?v=Ao9e0cDzMrE

You can find these on the resource page of the class website.

R Markdown files (.Rmd) help generate reports that include your code and output. Think of them as fancier scripts.

1. Helps you describe your code
2. Allows you to check the output
3. Can create many different file types

Go to File → New File → R Markdown or click the green add file button.

Within R Markdown files are code “chunks”

This is where you can type R code and run it!

To create a new R code chunk:

Copy paste an existing chunk in the R Markdown file and replace the code OR

1. Use the insert code chunk button at the top of RStudio.

1. Select R (default) as the language:

You can run all chunks above a specific chunk using this button:

You can specify if a chunk will be seen in the report or not.

This will create a report from the R Markdown document!

• Ctrl + Enter in your script evaluates that line of code
  • It’s like copying and pasting the code into the console for it to run.
• Ctrl+1 takes you to the script page
• Ctrl+2 takes you to the console
• http://www.rstudio.com/ide/docs/using/keyboard_shortcuts

In RStudio Click the Edit tab –> scroll down to Preferences… –> R Markdown

Uncheck the following:

• you can test code in the console

• you can save code in a chunk in the editor (Markdown file)

When you type in a function name, a pop up will preview documentation to help you. It also helps you remember the name of the function if you don’t remember all of it!

If you know the name of a package or function:

Type ?package_name or ?function_name in the console to get information about packages and functions.

For example: ?readr or ?read_csv.

If you haven’t loaded a package yet into R than you may get a response that there is no documentation.

Typing in ??package_name can show you packages that you haven’t loaded yet.

• RStudio makes working in R easier
• the Editor is for static code like scripts or R Markdown documents
• The console is for testing code
• R markdown documents are really helpful for lots of reasons!
• R code goes within what is called a chunk (the gray box with a green play button)
• Code chunks can be modified so that they show differently in reports

🏠 Class Website

💻 Lab

Image by Gerd Altmann from Pixabay